Contacts of the helix formed by residues 541 - 546 (chain A) in PDB entry 4KYI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 541 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ALA* 4.1 28.0 - - + +
332A ILE* 4.7 14.4 - - + -
335A PHE* 3.8 26.2 - - + -
539A TRP 3.6 0.2 - - - -
540A ALA* 1.3 84.2 - - + +
542A ILE* 1.3 60.4 + - - +
543A GLU* 4.3 7.6 - - + +
544A TRP* 2.9 42.6 + - + +
545A VAL* 3.3 10.0 - - - +
553A ALA* 4.7 8.5 - - + -
555A ASP* 4.6 11.2 - - + +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ALA* 5.5 0.6 - - - +
362A GLU* 3.5 29.8 + - + +
363A LYS 3.7 24.5 - - - +
364A VAL* 4.3 5.6 - - + -
422A TYR* 5.8 0.7 - - + -
498A LEU* 4.3 13.0 - - + -
501A LYS* 3.8 21.1 - - + +
540A ALA 3.3 4.8 + - - -
541A PRO* 1.3 70.6 - - - +
543A GLU* 1.3 64.0 + - - +
544A TRP 3.0 1.4 + - - -
545A VAL* 3.5 29.2 + - + +
546A VAL* 3.2 26.0 + - + +
604A GOL 3.3 30.4 + - - +
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ALA* 4.0 33.8 - - - +
331A ALA* 5.9 2.0 - - + -
332A ILE* 5.0 3.4 - - + +
541A PRO* 3.0 5.8 - - + -
542A ILE* 1.3 80.4 - - - +
544A TRP* 1.3 57.9 + - - +
546A VAL* 4.6 7.3 - - - +
547A SER* 3.5 17.2 + - - -
555A ASP* 4.0 17.6 - - - +
556A PHE 4.6 6.2 - - - +
557A LYS* 4.1 16.4 + - - +
604A GOL 4.3 20.2 - - - -
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Residues in contact with TRP 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ILE* 4.4 7.9 - - + -
493A GLU* 3.9 22.2 - - + -
494A LYS* 3.3 49.5 - - + +
497A ALA* 5.1 1.1 - - + -
537A LEU* 5.3 3.6 - - + -
540A ALA* 4.1 18.6 - - + -
541A PRO* 2.9 27.9 + - + +
543A GLU* 1.3 79.8 - - - +
545A VAL* 1.3 87.3 + - + +
546A VAL 3.3 2.5 - - - -
547A SER* 3.2 17.6 + - - -
549A PHE* 3.7 22.0 - + + -
551A GLY 2.9 26.0 + - - -
552A PRO* 3.8 7.1 + - + -
553A ALA* 4.0 23.1 - - + -
555A ASP* 3.8 20.6 - - + -
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Residues in contact with VAL 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A MET* 3.2 24.4 - - + +
494A LYS* 3.4 39.9 - - + +
497A ALA* 4.3 15.7 - - + -
498A LEU* 4.5 8.3 - - + -
501A LYS* 4.6 3.6 - - - -
540A ALA* 4.4 4.5 - - + -
541A PRO 3.3 18.8 - - - +
542A ILE* 3.6 30.1 - - + +
544A TRP* 1.3 96.8 - - + +
546A VAL* 1.3 68.5 + - + +
547A SER 3.3 1.7 + - - +
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A THR 5.1 0.3 - - - +
413A PHE* 4.1 17.2 - - + -
418A MET* 4.4 7.6 - - + -
422A TYR* 3.6 55.1 - - + +
498A LEU* 4.8 0.9 - - + -
542A ILE* 3.2 24.5 - - + +
543A GLU* 4.6 7.6 - - - +
545A VAL* 1.3 90.8 - - + +
547A SER* 1.3 63.4 + - - +
548A LEU* 4.5 4.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il